Liolaemus pictus is a widely distributed arboreal lizard species in southern Chile. Within this species, mainland and island subspecies have been described mainly based on external morphological characters, however, their diagnostic characters have not been accurately demarcated. We used both traditional and geometric morphometrics to study the morphological divergence in L. pictus subspecies. Since geographic isolation can be related to environmental variation (e.g., variation in abundance and richness of insects or fruits), we predict that the L. pictus morphology could vary in head shape between mainland and island localities. Our results show morphological divergence in all variables analyzed among the island and mainland localities. The traditional morphometric approach reveals differences between populations from the mainland and island localities, where the mainland populations show a larger head size. Geometric morphometric data indicate that the eye orbits of the island specimens are more extended than in the mainland specimens in the dorsal view; this is probably related to a different capacity of substrate used. Also, in the lateral view, the eye orbits are extended and the head shape is less dorso-ventrally compressed in the island locality than in mainland populations and the terminal mouth position is more posterior in island specimens. We suggest that the morphological variation between mainland and island localities could be related to the fact that these populations were isolated during the last maximum glacial period in southern Chile, a period in which geomorphologic and bioclimatic features of this area were modified forming the present archipelago.